The ATM repair pathway inhibits RNA polymerase I transcription in response to chromosome breaks

Abstract

DNA lesions interfere with DNA and RNA polymerase activity. Cyclobutane pyrimidine dimers and photoproducts generated by ultraviolet irradiation cause stalling of RNA polymerase II, activation of transcription-coupled repair enzymes, and inhibition of RNA synthesis. During the S phase of the cell cycle, collision of replication forks with damaged DNA blocks ongoing DNA replication while also triggering a biochemical signal that suppresses the firing of distant origins of replication. Whether the transcription machinery is affected by the presence of DNA double-strand breaks remains a long-standing question. Here we monitor RNA polymerase I (Pol I) activity in mouse cells exposed to genotoxic stress and show that induction of DNA breaks leads to a transient repression in Pol I transcription. Surprisingly, we find Pol I inhibition is not itself the direct result of DNA damage but is mediated by ATM kinase activity and the repair factor proteins NBS1 (also known as NLRP2) and MDC1. Using live-cell imaging, laser micro-irradiation, and photobleaching technology we demonstrate that DNA lesions interfere with Pol I initiation complex assembly and lead to a premature displacement of elongating holoenzymes from ribosomal DNA. Our data reveal a novel ATM/NBS1/MDC1-dependent pathway that shuts down ribosomal gene transcription in response to chromosome breaks.

Emerging Roles of the Nucleolus in Regulating the DNA Damage Response: The Noncanonical DNA Repair Enzyme APE1/Ref-1 as a Paradigmatical Example

“…Concurrently, also DNA repair factors stored within nucleoli and frequently bound to NCL and NPM1 are released into the nucleoplasm; the transient arrest of the cell-cycle progression possibly facilitates the DNA repair process. Only after resolution of DNA damage, rRNA synthesis is restored, as suggested by the inverse correlation existing between the rDNA transcription rate and c-H2AX foci number (80). Notably, many nucleolar effectors also play a role within the nucleoplasm: beside the contribution to the modulation of the cell-cycle, several reports have pointed out that NCL or NPM1 may directly participate in the DDR.…”

“…In addition, the nucleolus has been reported to contain several DNA damage sensors (e.g., the ataxia telangiectasia mutated [ATM], the ataxia telangiectasia and Rad3-related [ATR], and p53) (5,123) and it has been demonstrated that, upon DNA damage induction, Pol I-mediated transcription is blocked in an ATM-dependent manner, and not by the DNA damage itself. Interestingly, through microirradiation studies, Kruhlak et al showed that transcription of rDNA is transiently arrested only in damaged nucleoli, whereas the neighboring ones maintain normal transcriptional activity (80). Moreover, Rubbi and Milner, have elegantly shown that nucleolar disruption, rather than DNA damage, may lead to p53 stabilization, suggesting that the nucleolus may constitutively promote p53 degradation, unless DNA damage occurs (124).…”

ATM-dependent E2F1 accumulation in the nucleolus is an indicator of ribosomal stress in early response to DNA damage

“…14,15,28 DNA damage results in a transient repression of rRNA transcription and a temporary cessation of DNA replication. 25 We found that pretreatment of cells with the specific ATM inhibitor KU55933 could abrogate ADR-inhibited transcription initiation of the rRNA gene (Fig. 6B).…”

“…25 To investigate the inhibition of rRNA transcription in ADR-induced DNA damage, we performed northern blot using ITS-1 and ITS-2 as hybridization probes (Fig. 6A).…”

“…10,[23][24][25] Induction of DNA breaks leads to a transient repression in Pol I transcription and a temporary cessation in DNA replication. 25 The studies of the correlation of DNA damage with the nucleolus have shown that the nucleolus acts as a sensor for cellular stress signals through stabilization of p53 by RP-Mdm2/ HDM2 and ARF-Mdm2/HDM2 interactions, which induces cell cycle arrest or apoptosis. 10,12,[20][21][22][23] Likewise, E2F1 as a DNA damage-responsive protein also plays roles in response to DNA damage through transcriptional response and protein-protein interaction.…”